NHK has learned that Russia denied permission for remains collected in the country's Far East to be brought to Japan for DNA testing.
Russia recently returned the remains of 18 people found in Sakhalin and on Shumshu Island. Seven of them have been visually identified as Japanese. The identity of the others has yet to be determined.
Japanese welfare ministry officials had planned to bring samples of the unidentified remains back to Japan for DNA tests.
The ministry decided to do this after a possible mix-up of remains of Japanese post-war internees in Siberia came to light.
But Russian officials reportedly cited legal problems with bringing the remains out of the country before they are confirmed to be those of Japanese.
The unidentified remains are expected to be temporarily stored at a museum in Sakhalin.
Japanese officials say they will discuss the matter with the Russian foreign ministry.